Molecular characterization reveals chlorosis-corrected CMS (Brassica oxyrrhina) B. juncea cybrid has recombinant mitochondrial genome involving male sterility inducing orf108-atpA gene

This study provides insights into the flexibility of the mitochondrial genome in sunflower (Helianthus annuus L.) as well as into the causes of ANN2-type cytoplasmic male sterility (CMS). De novo assembly of the mitochondrial genome of male-sterile HA89(ANN2) sunflower line was performed using high-throughput sequencing technologies. Analysis of CMS ANN2 mitochondrial DNA sequence revealed the following reorganization events: twelve rearrangements, seven insertions, and nine deletions. Comparisons of coding sequences from the male-sterile line with the male-fertile line identified a deletion of orf777 and seven new transcriptionally active open reading frames (ORFs): orf324, orf327, orf345, orf558, orf891, orf933, orf1197. Three of these ORFs represent chimeric genes involving atp6 (orf1197), cox2 (orf558), and nad6 (orf891). In addition, orf558, orf891, orf1197, as well as orf933, encode proteins containing membrane domain(s), making them the most likely candidate genes for CMS development in ANN2. Although the investigated CMS phenotype may be caused by simultaneous action of several candidate genes, we assume that orf1197 plays a major role in developing male sterility in ANN2. Comparative analysis of mitogenome organization in sunflower lines representing different CMS sources also allowed identification of reorganization hot spots in the mitochondrial genome of sunflower.

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Candidate Gene Selection for Cytoplasmic Male Sterility in Pepper (Capsicum annuum L.) through Whole Mitochondrial Genome Sequencing

International Journal of Molecular Sciences ◽

10.3390/ijms20030578 ◽

2019 ◽

Vol 20 (3) ◽

pp. 578 ◽

Cited By ~ 9

Author(s):

Peng Wang ◽

Qiaohua Lu ◽

Yixin Ai ◽

Yihao Wang ◽

Tiantian Li ◽

...

Keyword(s):

Mitochondrial Genome ◽

Cytoplasmic Male Sterility ◽

Candidate Gene ◽

Male Sterility ◽

Gene Selection ◽

Transmembrane Domain ◽

Genome Structure ◽

Potential Candidate ◽

Hybrid Seed Production ◽

Cms Line

Cytoplasmic male sterility (CMS), which is controlled by mitochondrial genes, is an important trait for commercial hybrid seed production. So far, genes controlling this trait are still not clear in pepper. In this study, complete mitochondrial genomes were sequenced and assembled for the CMS line 138A and its maintainer line 138B. The genome size of 138A is 504,210 bp, which is 8618 bp shorter than that of 138B. Meanwhile, more than 214 and 215 open reading frames longer than 100 amino acids (aas) were identified in 138A and 138B, respectively. Mitochondrial genome structure of 138A was quite different from that of 138B, indicating the existence of recombination and rearrangement events. Based on the mitochondrial genome sequence and structure variations, mitochondrion of 138A and FS4401, a Korean origin CMS line, may have inherited from a common female ancestor, but their CMS traits did originate separately. Candidate gene selection was performed according to the published characteristics of the CMS genes, including the presence SNPs and InDels, located in unique regions, their chimeric structure, co-transcription, and transmembrane domain. A total of 35 ORFs were considered as potential candidate genes and 14 of these were selected, with orf300a and 0rf314a as strong candidates. A new marker, orf300a, was developed which did co-segregate with the CMS trait.

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Cytoplasmic Male Sterility and Mitochondrial Genome Variations in Radish

Compendium of Plant Genomes - The Radish Genome ◽

10.1007/978-3-319-59253-4_7 ◽

2017 ◽

pp. 93-108 ◽

Cited By ~ 1

Author(s):

Hiroshi Yamagishi ◽

Toru Terachi

Keyword(s):

Mitochondrial Genome ◽

Cytoplasmic Male Sterility ◽

Male Sterility ◽

Genome Variations

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Organelle genome composition and candidate gene identification for Nsa cytoplasmic male sterility in Brassica napus

BMC Genomics ◽

10.1186/s12864-019-6187-y ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 2

Author(s):

Shi-Fei Sang ◽

De-Sheng Mei ◽

Jia Liu ◽

Qamar U. Zaman ◽

Hai-Yan Zhang ◽

...

Keyword(s):

Brassica Napus ◽

Mitochondrial Genome ◽

Cytoplasmic Male Sterility ◽

Male Sterility ◽

Parental Species ◽

Sequencing Technology ◽

Genome Composition ◽

Maintainer Line ◽

Organelle Genomes ◽

Cms Line

Abstract Background Nsa cytoplasmic male sterility (CMS) is a novel alloplasmic male sterility system derived from somatic hybridization between Brassica napus and Sinapis arvensis. Identification of the CMS-associated gene is a prerequisite for a better understanding of the origin and molecular mechanism of this CMS. With the development of genome sequencing technology, organelle genomes of Nsa CMS line and its maintainer line were sequenced by pyro-sequencing technology, and comparative analysis of the organelle genomes was carried out to characterize the organelle genome composition of Nsa CMS as well as to identify the candidate Nsa CMS-associated genes. Results Nsa CMS mitochondrial genome showed a higher collinearity with that of S. arvensis than B. napus, indicating that Nsa CMS mitochondrial genome was mainly derived from S. arvensis. However, mitochondrial genome recombination of parental lines was clearly detected. In contrast, the chloroplast genome of Nsa CMS was highly collinear with its B. napus parent, without any evidence of recombination of the two parental chloroplast genomes or integration from S. arvensis. There were 16 open reading frames (ORFs) specifically existed in Nsa CMS mitochondrial genome, which could not be identified in the maintainer line. Among them, three ORFs (orf224, orf309, orf346) possessing chimeric and transmembrane structure are most likely to be the candidate CMS genes. Sequences of all three candidate CMS genes in Nsa CMS line were found to be 100% identical with those from S. arvensis mitochondrial genome. Phylogenetic and homologous analysis showed that all the mitochondrial genes were highly conserved during evolution. Conclusions Nsa CMS contains a recombined mitochondrial genome of its two parental species with the majority form S. arvensis. Three candidate Nsa CMS genes were identified and proven to be derived from S. arvensis other than recombination of its two parental species. Further functional study of the candidate genes will help to identify the gene responsible for the CMS and the underlying molecular mechanism.

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Variation in plastid genomes in the gynodioecious species Silene vulgaris

BMC Plant Biology ◽

10.1186/s12870-019-2193-0 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 5

Author(s):

Manuela Krüger ◽

Oushadee A. J. Abeyawardana ◽

Miloslav Juříček ◽

Claudia Krüger ◽

Helena Štorchová

Keyword(s):

Gene Expression ◽

Mitochondrial Genome ◽

Male Sterility ◽

Higher Plants ◽

Complete Mitochondrial Genome ◽

Specific Gene ◽

Silene Vulgaris ◽

Male Sterile ◽

Genome Sequences ◽

Plastid Genomes

Abstract Background Gynodioecious species exist in two sexes – male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(s) encoded by mitochondrial genome and by nuclear-encoded restorer genes. Mitochondrial and nuclear-encoded transcriptomes in females and hermaphrodites are intensively studied, but little is known about sex-specific gene expression in plastids. We have compared plastid transcriptomes between females and hermaphrodites in two haplotypes of a gynodioecious species Silene vulgaris with known CMS candidate genes. Results We generated complete plastid genome sequences from five haplotypes S. vulgaris including the haplotypes KRA and KOV, for which complete mitochondrial genome sequences were already published. We constructed a phylogenetic tree based on plastid sequences of S. vulgaris. Whereas lowland S. vulgaris haplotypes including KRA and KOV clustered together, the accessions from high European mountains diverged early in the phylogram. S. vulgaris belongs among Silene species with slowly evolving plastid genomes, but we still detected 212 substitutions and 112 indels between two accessions of this species. We estimated elevated Ka/Ks in the ndhF gene, which may reflect the adaptation of S. vulgaris to high altitudes, or relaxed selection. We compared depth of coverage and editing rates between female and hermaphrodite plastid transcriptomes and found no significant differences between the two sexes. We identified 51 unique C to U editing sites in the plastid genomes of S. vulgaris, 38 of them in protein coding regions, 2 in introns, and 11 in intergenic regions. The editing site in the psbZ gene was edited only in one of two plastid genomes under study. Conclusions We revealed no significant differences between the sexes in plastid transcriptomes of two haplotypes of S. vulgaris. It suggests that gene expression of plastid genes is not affected by CMS in flower buds of S. vulgaris, although both sexes may still differ in plastid gene expression in specific tissues. We revealed the difference between the plastid transcriptomes of two S. vulgaris haplotypes in editing rate and in the coverage of several antisense transcripts. Our results document the variation in plastid genomes and transcriptomes in S. vulgaris.

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